Bottom Line:
In addition, the communities were also completely different from other microbial communities sequenced to date.We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages.Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Affiliation: Department of Biology, San Diego State University, San Diego, USA. redwards@salmonella.org

ABSTRACT

Background: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.

Results: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.

Conclusion: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Figure 6: Respiration in aerobic and anaerobic environments. Among other potential pathways in the Soudan mine, electrons are transferred from hydrogenases to either cytochromes and then to oxygen to produce water in an oxidative environment, or via nitrate and nitrite reductases (denitrification) in anaerobic environments. Genes encoding the hydrogenases, respiratory complexes, and terminal cytochromes of the aerobic sample were significantly more abundant in the Red (oxidized) sample, while genes encoding the hydrogenases and denitrification genes were more abundant in the Black (reduced) sample. After Vassieva, O. [25]

Mentions:
The respiratory complexes and cytochrome-C oxidases are more commonly found in the sample from the oxidized environment (the Red sample; Table 2). Respiration proceeds via multiple electron transfer steps (Figure 6). In an aerobic environment, electrons are passed from hydrogenases to quinones (e.g., ubiquinone, quinone, menaquinone, and plastoquinone) and then to cytochromes resulting in the conversion of oxygen to water. In anaerobic environments the electrons are shuffled through nitrite and nitrate reductases, reducing NO3 first to NO2 and then to N2 gas. The Black sample is enriched for these denitrification genes suggesting that the latter pathway predominates while the Red sample is enriched for components of the aerobic respiratory pathway. Moreover, the Black sample had a lower concentration of free nitrate than the Red sample, presumably because nitrate is being used as an electron acceptor during respiration (although nitrite was below the level of detection in both samples; Table 3).

Figure 6: Respiration in aerobic and anaerobic environments. Among other potential pathways in the Soudan mine, electrons are transferred from hydrogenases to either cytochromes and then to oxygen to produce water in an oxidative environment, or via nitrate and nitrite reductases (denitrification) in anaerobic environments. Genes encoding the hydrogenases, respiratory complexes, and terminal cytochromes of the aerobic sample were significantly more abundant in the Red (oxidized) sample, while genes encoding the hydrogenases and denitrification genes were more abundant in the Black (reduced) sample. After Vassieva, O. [25]

Mentions:
The respiratory complexes and cytochrome-C oxidases are more commonly found in the sample from the oxidized environment (the Red sample; Table 2). Respiration proceeds via multiple electron transfer steps (Figure 6). In an aerobic environment, electrons are passed from hydrogenases to quinones (e.g., ubiquinone, quinone, menaquinone, and plastoquinone) and then to cytochromes resulting in the conversion of oxygen to water. In anaerobic environments the electrons are shuffled through nitrite and nitrate reductases, reducing NO3 first to NO2 and then to N2 gas. The Black sample is enriched for these denitrification genes suggesting that the latter pathway predominates while the Red sample is enriched for components of the aerobic respiratory pathway. Moreover, the Black sample had a lower concentration of free nitrate than the Red sample, presumably because nitrate is being used as an electron acceptor during respiration (although nitrite was below the level of detection in both samples; Table 3).

Bottom Line:
In addition, the communities were also completely different from other microbial communities sequenced to date.We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages.Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.

Affiliation:
Department of Biology, San Diego State University, San Diego, USA. redwards@salmonella.org

ABSTRACT

Background: Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.

Results: Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.

Conclusion: We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.